HumanGenomeDating
Atlas of Variant Age
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Examples: LCT, MCM6, EDAR, ZEB1
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Populations: 26
Individuals: 2,535
Ancestry analyses:565,507,800
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SGDP
Simons Genome Diversity Project
Populations: 130
Individuals: 278
Ancestry analyses:6,800,992
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Genealogical Estimation of Variant Age (GEVA)

Inference of the ancestral origin of a genetic variant at a single locus

rs372508878
Alleles:
reference
C
ancestral
alternate
T
derived
Age estimated for the alternate allele, assuming that it was derived from the reference allele as the ancestral state.
How was the ancestral/derived state determined?Chromosome 2   position  136,564,601  (GRCh37) Explore rs372508878 on Ensembl!
Allele frequency in   SGDP ⇪
Sample 98.9%
1.1%
AFR 93.2%
6.8%
AMR 100.0%
0.0%
CAS 100.0%
0.0%
EAS 100.0%
0.0%
OCN 100.0%
0.0%
SAS 100.0%
0.0%
WEA 100.0%
0.0%
reference ← allele frequency → alternate
Select clock model
  Mutation clock
  Recombination clock
  Joint clock
Age estimation summary Joint clock
Data source Estimated age of T allele # pairs = concordant + discordant Quality score
    Genomes in SGDP10,085.9 generations 107  =  8  +  990.970
Pairwise results table Joint clock
Haplotype pair Pair type Data source Breakpoint positions Physical length (bp) Genetic Length (cM) α β Mean TMRCA (generations)
S_Mandenka-2A + S_Khomani_San-1B Concordant SGDP 136,494,791 – 136,602,042 107,250.5 0.01678074 24 65.9048 7,283.2
S_Mandenka-2B + S_Khomani_San-1A Concordant SGDP 136,556,012 – 136,565,535 9,523.0 0.00304087 3 8.0037 7,496.5
S_Ju_hoan_North-1B + S_Khomani_San-1B Concordant SGDP 135,436,058 – 136,772,749 1,336,691.0 0.36529398 178 934.8469 3,808.1
S_Ju_hoan_North-1B + S_Mandenka-2A Concordant SGDP 136,494,791 – 136,602,042 107,250.5 0.01678074 23 65.9048 6,979.8
S_BantuTswana-2B + S_Khomani_San-1A Concordant SGDP 136,555,141 – 136,566,474 11,333.0 0.00454331 3 10.0745 5,955.6
S_Mandenka-2B + S_Khomani_San-1B Concordant SGDP 136,556,012 – 136,565,535 9,523.0 0.00304087 3 8.0037 7,496.5
S_BantuTswana-2B + S_Mandenka-2B Concordant SGDP 136,556,012 – 136,646,325 90,312.5 0.01676442 24 57.7615 8,310.0
S_BantuTswana-2B + S_Ju_hoan_North-1B Concordant SGDP 136,555,141 – 136,632,444 77,302.5 0.01599323 17 50.8998 6,679.8
S_Khomani_San-1B + S_Saami-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Greek-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Punjabi-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Estonian-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Mandenka-2A + S_Dusun-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Dai-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Saharawi-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + B_Ju_hoan_North-4A Discordant SGDP 135,437,187 – 136,572,640 1,135,453.0 0.33627945 273 815.0410 6,699.0
S_Khomani_San-1A + S_Ju_hoan_North-2B Discordant SGDP 136,411,978 – 136,787,291 375,313.0 0.07797775 33 243.5324 2,710.1
S_Khomani_San-1A + S_Turkish-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Mandenka-2A + S_Dinka-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Mandenka-2A + S_Yoruba-1B Discordant SGDP 136,556,012 – 136,564,602 8,590.0 0.00300843 4 7.5299 10,624.2
S_Mandenka-2A + S_Czech-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Norwegian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Tlingit-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Turkish-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Miao-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Mandenka-2B + S_Uygur-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Mandenka-2A + S_Naxi-1A Discordant SGDP 135,760,098 – 136,564,602 804,504.5 0.06697593 88 440.7429 3,993.3
S_Khomani_San-1A + S_Spanish-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Mandenka-2B + S_Dai-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Yemenite_Jew-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Mandenka-2B + S_Kinh-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Piapoco-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Mandenka-2B + S_Kusunda-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Cambodian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Mandenka-2B + S_Burusho-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Xibo-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Mandenka-2B + S_Luhya-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Kinh-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Mandenka-2B + S_Bulgarian-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Atayal-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Mandenka-2B + S_Lezgin-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Finnish-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Mandenka-2B + S_Mende-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Basque-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Mozabite-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Druze-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Mixe-3A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_North_Ossetian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Mongola-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + B_Crete-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Mongola-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Pima-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Tubalar-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Adygei-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Naxi-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Adygei-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Miao-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Tajik-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Hezhen-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Turkish-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Thai-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + B_Sardinian-3B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Chukchi-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Karitiana-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Mozabite-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Mixtec-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Mansi-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Aleut-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Brahmin-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Dai-3B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Hazara-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Daur-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Punjabi-4B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Yi-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Czech-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Xibo-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_English-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Sindhi-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_English-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Bulgarian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_BantuKenya-1A Discordant SGDP 136,556,012 – 136,564,602 8,590.0 0.00300843 5 7.5299 13,280.3
S_Khomani_San-1B + S_English-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Estonian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Estonian-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Finnish-3A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Finnish-3B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Saami-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_French-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_French-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Georgian-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Basque-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Icelandic-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Icelandic-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Kyrgyz-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Iranian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Ju_hoan_North-3B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Samaritan-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Ju_hoan_North-1A Discordant SGDP 136,559,711 – 136,572,640 12,929.0 0.00056393 5 7.6571 13,059.8
S_Khomani_San-1A + S_Tuscan-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Yemenite_Jew-2B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Jordanian-3B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + B_French-3B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Norwegian-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Piapoco-1B Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Orcadian-1A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1B + S_Pima-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
S_Khomani_San-1A + S_Orcadian-2A Discordant SGDP 136,564,590 – 136,564,602 12.5 0.00000044 4 1.0063 79,495.4
View as figure
Data shown in this table can be downloaded from this page.
α Shape parameter of the Gamma distribution, calculated from the number of pairwise differences along the sequence of the inferred shared haplotype segment (mutation clock), or the breakpoints detected (recombination clock), or both (joint clock); plus the parameter of the coalescent prior distribution (equal to 1 by default).
β Rate parameter of the Gamma distribution, calculated from the physical length of the inferred shared haplotype segment and the mutation rate (mutation clock), or the genetic length given the variable recombination rate (recombination clock), or both (joint clock); plus the parameter of the coalescent prior distribution (equal to 1 by default).
Mean TMRCA Calculated as the mean of the Gamma distribution with parameters α and β, multiplied by 2 x Ne, where Ne = 10,000 by default.
 

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